https://github.com/cafferychen777/easymicrobiome

https://github.com/cafferychen777/easymicrobiome

Repository

https://github.com/cafferychen777/EasyMicrobiome/blob/master/

# (EasyMicrobiome)



Popular software, scripts and database annotation for EasyAmplicon and EasyMetagenome

(Version)EasyMicrobiome v1.16

(Update)2022/8/18

(Project homepage): https://github.com/yongxinliu/EasyMicrobiome

## (Install)






	# 1. gitwget
	git clone https://github.com/YongxinLiu/EasyMicrobiome

	# 2. 
	wget -c http://210.75.224.110/db/EasyMicrobiome.zip
	unzip EasyMicrobiome.zip

linux

	chmod +x EasyMicrobiome/linux/*



	# 
	export PATH=$PATH:`pwd`/EasyMicrobiome/linux:`pwd`/EasyMicrobiome/script"
	# .bashrc
	echo "PATH=$PATH:`pwd`/EasyMicrobiome/linux:`pwd`/EasyMicrobiome/script" >> ~/.bashrc

## 



- https://github.com/YongxinLiu/EasyAmplicon

- https://github.com/YongxinLiu/EasyMetagenome

RWindows(R)4

- R4.2RR http://www.r-project.org Windows http://210.75.224.110/db/train/2107Amplicon12/win_soft/4.2.zip

## 

*

- linuxLinux
    - [microbiome_helper](https://github.com/LangilleLab/microbiome_helper)metaphlan2STAMP(metaphlan_to_stamp.pl)picurst(plot_metagenome_contributions.R)
    - Miniconda2-latest-Linux-x86_64.sh https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
    - qiime2-2022.2.tar.gzQIIME2condaenvs http://210.75.224.110/db/conda/qiime2-2022.2.tar.gz
    - qiime2-2022.2-py36-linux-conda.ymlQIIME2conda
    - [sparcc](https://github.com/TankMermaid/sparcc)sparccpython
    - [usearch](http://www.drive5.com/usearch/)
    - [vsearch](https://github.com/torognes/vsearch)(64usearch)
- macMac
    - csvtk
    - iqtree
    - qiime2-2022.2-py36-osx-conda.ymlQIIME2conda
    - R-4.2.0.pkgR
    - RStudio-1.4.1106.dmgRStudio
    - rush
    - seqkit
    - taxonkitNCBI
    - usearch
    - vsearch(64usearch)
- winWindows
    - [Git-2.30.2-64-bit.exe](http://gitforwindows.org/)Git bash[Windowslinux shellgitforwindows](https://mp.weixin.qq.com/s/KtM4c4o4iLfD4ZkEnMi1pg)
    - [R-4.2.0-win.exe](https://www.r-project.org/ )RDownad CRAN - China Tsinghua - Download R for Windows(Mac)  base  Download R 4.2.0
    - [RStudio-1.4.1106.exe](https://www.rstudio.com/products/rstudio/download/#download)RStudio
    - [4.2.zip](http://210.75.224.110/db/R/4.2.zip)R400+R
    - [usearch.exe](http://www.drive5.com/usearch/)
    - [vsearch.exe](https://github.com/torognes/vsearch)(64usearch)
    - [STAMP2.1.3](http://kiwi.cs.dal.ca/Software/STAMP)
    - Adobe_Illustrator_CC_2018_v22.1.0.314_x64_zh_CN_Portable.7z
    - [Cytoscape_3_8_2_windows_64bit.exe](http://www.cytoscape.org)
    - [csvtk.exe](https://github.com/shenwei356/csvtk)
    - [seqkit.exe](https://github.com/shenwei356/seqkit)
    - [taxonkit.exe](https://github.com/shenwei356/taxonkit )NCBI
    - [rush.exe](https://github.com/shenwei356/rush)
    - [epp510_1828_64bit.exe](https://www.editplus.com/)
    - [Xshell](https://www.netsarang.com/zh/free-for-home-school)[PuTTY](http://www.putty.be/)
    - [FileZilla](https://filezilla-project.org/download.php?type=client)[WinSCP](https://winscp.net/eng/download.php)
    - [gephi-0.9.2-windows.exe](https://gephi.org/)
    - iqtree.exe
    - libiomp5md.dlliqtree
    - jdk-11.0.7_windows-x64_bin.exeJava
    - muscle.exe
    - npp.7.8.9.Installer.x64.exeNotePad++
    - rtools40-x86_64.exeR
    - wget.exe

## 

- ggGreenGenes16S
    - [gg_13_8_otus.tar.gz](ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_8_otus.tar.gz
)138OTUusearchPICRUSt/BugBaseQIIME 2[](http://210.75.224.110/db/gg/gg_13_8_otus.tar.gz)
    - [16S_13_5_precalculated.tab.gz](http://210.75.224.110/db/picrust/16S_13_5_precalculated.tab.gz)picrustGreenGenes 16S
	- [ko_13_5_precalculated.tab.gz](http://210.75.224.110/db/picrust/ko_13_5_precalculated.tab.gz)picrustGreenGenes 16SKO
- keggKEGG
    - [ko00001.keg](https://www.kegg.jp)KEGG  KEGG BRITE  KEGG Orthology (KO)  Download htextko00001.tsv
    - ko00001.tsvjasonKO()
    - KO1-4.txtKO3()KO
    - KO_description.txtKO
    - KO_path.listKO(Pathway)KO(1)
- usearchusearch/vsearchsintax
    - [rdp_16s_v16_sp.fa.gz](http://www.drive5.com/usearch/manual/sintax_downloads.html)16SRDP16usearch16SITS18S http://www.drive5.com/usearch/manual/sintax_downloads.html
    - rdp_16s_v18.fa.gz16SRDP182021RDP
    - utax_reference_dataset_all_04.02.2020.fasta.gzITSUNITE
- eggnog: eggnog
    - COG.annoCOG

##  

- 
    - .RRRscript
    - .shShell/bin/bash
    - .plPerlperl
    - .pyPythonpythonpython2python3

- script
    - BugBase16SR
    - FAPROTAX_1.2.416SPython
    - table2itoliTOLR
    - alpha_barplot.RAlpha+
    - alpha_boxplot.RAlpha+
    - alpha_rare_curve.Rusearch
    - beta_cpcoa.RPCoA++3
    - beta_pcoa.RPCoA+++
    - BetaDiv.RBetaPCAPCoANMDSLDACCARDA
    - compare.Rt.testwilcoxedgeR
    - compare_heatmap.R/sh
    - compare_manhattan.sh
    - compare_volcano.R
    - faprotax_report_sum.plFARPROTAX
    - filter_feature_table.ROTU
    - format_dbcan2list.pldbcan
    - format2lefse.ROTULEfSe
    - format2stamp.ROTUSTAMP
    - kegg_ko00001_htext2tsv.plKEGG
    - kraken2alpha.RKraken2alpha
    - mat_gene2ko.R
    - metaphlan_boxplot.Rmetaphalan2
    - metaphlan_hclust_heatmap.Rmetaphalan2
    - metaphlan_to_stamp.plmetaphalan2STAMP
    - otu_mean.ROTU()
    - otutab_filter_nonBac.R16SOTUsintax
    - otutab_filter_nonFungi.RITSOTU
    - otutab_freq2count.RedgeR
    - otutab_rare.ROTU
    - plot_metagenome_contributions.RPICRUSt
    - sp_pheatmap.sh
    - sp_vennDiagram.sh
    - summarizeAbundance.pyKEGGKO
    - tax_circlize.R
    - tax_maptree.R
    - tax_stackplot.R



If used this script, please cited:

Tong Chen, Yong-Xin Liu, Luqi Huang. 2022. ImageGP: An easy-to-use data visualization web server for scientific researchers. iMeta 1: e5. https://doi.org/10.1002/imt2.5

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai. 2021. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein & Cell 12: 315-330. https://doi.org/10.1007/s13238-020-00724-8

Copyright 2016-2022 Yong-Xin Liu , Tong Chen

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